[2024-01-24 13:31:33,081] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,084] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,085] [INFO] DQC Reference Directory: /var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference
[2024-01-24 13:31:34,394] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,395] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,395] [INFO] Running command: gunzip -c /var/lib/cwl/stga950e916-42c7-406c-a500-97e5c5f7e5c1/GCF_014635545.1_ASM1463554v1_genomic.fna.gz | prodigal -d GCF_014635545.1_ASM1463554v1_genomic.fna/cds.fna -a GCF_014635545.1_ASM1463554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:44,718] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:44,719] [INFO] Task started: HMMsearch
[2024-01-24 13:31:44,719] [INFO] Running command: hmmsearch --tblout GCF_014635545.1_ASM1463554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference/reference_markers.hmm GCF_014635545.1_ASM1463554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:45,035] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:45,037] [INFO] Found 6/6 markers.
[2024-01-24 13:31:45,073] [INFO] Query marker FASTA was written to GCF_014635545.1_ASM1463554v1_genomic.fna/markers.fasta
[2024-01-24 13:31:45,073] [INFO] Task started: Blastn
[2024-01-24 13:31:45,074] [INFO] Running command: blastn -query GCF_014635545.1_ASM1463554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference/reference_markers.fasta -out GCF_014635545.1_ASM1463554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:45,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:45,828] [INFO] Selected 19 target genomes.
[2024-01-24 13:31:45,828] [INFO] Target genome list was writen to GCF_014635545.1_ASM1463554v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:45,844] [INFO] Task started: fastANI
[2024-01-24 13:31:45,844] [INFO] Running command: fastANI --query /var/lib/cwl/stga950e916-42c7-406c-a500-97e5c5f7e5c1/GCF_014635545.1_ASM1463554v1_genomic.fna.gz --refList GCF_014635545.1_ASM1463554v1_genomic.fna/target_genomes.txt --output GCF_014635545.1_ASM1463554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:01,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:01,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:01,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:01,424] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:32:01,424] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:01,424] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Acinetobacter courvalinii	strain=CCM 8635	GCA_014635545.1	280147	280147	type	True	100.0	1299	1301	95	conclusive
Acinetobacter courvalinii	strain=CCUG 67960	GCA_008802255.1	280147	280147	type	True	99.9992	1297	1301	95	conclusive
Acinetobacter vivianii	strain=CCM 8642	GCA_014635885.1	1776742	1776742	type	True	90.1213	1096	1301	95	below_threshold
Acinetobacter proteolyticus	strain=NIPH 809	GCA_000367945.1	1776741	1776741	type	True	86.111	977	1301	95	below_threshold
Acinetobacter gyllenbergii	strain=MTCC 11365	GCA_000414075.1	134534	134534	type	True	85.4373	985	1301	95	below_threshold
Acinetobacter gyllenbergii	strain=CIP 110306	GCA_000413855.1	134534	134534	type	True	85.3966	986	1301	95	below_threshold
Acinetobacter colistiniresistens	strain=NIPH 2036	GCA_000413935.1	280145	280145	type	True	85.1884	927	1301	95	below_threshold
Acinetobacter venetianus	strain=RAG-1	GCA_000271425.1	52133	52133	type	True	82.9522	706	1301	95	below_threshold
Acinetobacter venetianus	strain=CIP 110063	GCA_000368585.1	52133	52133	type	True	82.8257	734	1301	95	below_threshold
Acinetobacter tjernbergiae	strain=DSM 14971	GCA_000374425.1	202955	202955	type	True	82.8217	734	1301	95	below_threshold
Acinetobacter tjernbergiae	strain=CIP 107465	GCA_000488175.1	202955	202955	type	True	82.8137	733	1301	95	below_threshold
Acinetobacter haemolyticus	strain=MTCC 9819	GCA_000430205.1	29430	29430	type	True	82.4352	650	1301	95	below_threshold
Acinetobacter haemolyticus	strain=NCTC10305	GCA_900444835.1	29430	29430	type	True	82.3965	681	1301	95	below_threshold
Acinetobacter haemolyticus	strain=CIP 64.3	GCA_000369065.1	29430	29430	type	True	82.3636	685	1301	95	below_threshold
Acinetobacter haemolyticus	strain=FDAARGOS_1392	GCA_019355995.1	29430	29430	type	True	82.2996	691	1301	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	82.1731	644	1301	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	80.0359	515	1301	95	below_threshold
Acinetobacter baumannii	strain=ATCC 19606	GCA_020911985.1	470	470	type	True	79.9597	517	1301	95	below_threshold
Acinetobacter baumannii	strain=PartI-Abaumannii-RM8376	GCA_022870045.1	470	470	type	True	79.9353	520	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:01,426] [INFO] DFAST Taxonomy check result was written to GCF_014635545.1_ASM1463554v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:01,427] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:01,427] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:01,427] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference/checkm_data
[2024-01-24 13:32:01,429] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:01,470] [INFO] Task started: CheckM
[2024-01-24 13:32:01,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635545.1_ASM1463554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635545.1_ASM1463554v1_genomic.fna/checkm_input GCF_014635545.1_ASM1463554v1_genomic.fna/checkm_result
[2024-01-24 13:32:36,063] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:36,064] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:36,081] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:36,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:36,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635545.1_ASM1463554v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:36,082] [INFO] Task started: Blastn
[2024-01-24 13:32:36,082] [INFO] Running command: blastn -query GCF_014635545.1_ASM1463554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg650d6bd6-cfa4-4512-8c4a-6a5c18785f73/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635545.1_ASM1463554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:37,210] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:37,213] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:37,213] [INFO] Target genome list was writen to GCF_014635545.1_ASM1463554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:37,243] [INFO] Task started: fastANI
[2024-01-24 13:32:37,243] [INFO] Running command: fastANI --query /var/lib/cwl/stga950e916-42c7-406c-a500-97e5c5f7e5c1/GCF_014635545.1_ASM1463554v1_genomic.fna.gz --refList GCF_014635545.1_ASM1463554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635545.1_ASM1463554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:49,955] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:49,966] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:49,966] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014635545.1	s__Acinetobacter courvalinii	100.0	1299	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.40	96.40	0.91	0.86	14	conclusive
GCF_014635885.1	s__Acinetobacter vivianii	90.1213	1096	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.48	96.89	0.92	0.86	8	-
GCF_000805455.1	s__Acinetobacter sp000805455	88.003	1021	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367945.1	s__Acinetobacter proteolyticus	86.111	977	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.84	97.76	0.89	0.87	5	-
GCF_009884975.1	s__Acinetobacter dispersus	85.7762	985	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.44	95.54	0.90	0.89	4	-
GCF_000369525.1	s__Acinetobacter sp000369525	85.7312	991	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.13	96.00	0.90	0.87	7	-
GCF_000413855.1	s__Acinetobacter gyllenbergii	85.4078	984	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.05	97.97	0.95	0.91	6	-
GCF_013072695.1	s__Acinetobacter sp013072695	85.3047	970	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369645.1	s__Acinetobacter sp000369645	85.2956	936	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.86	98.16	0.89	0.84	9	-
GCF_000413935.1	s__Acinetobacter colistiniresistens	85.1632	929	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.98	96.69	0.90	0.86	10	-
GCF_000368585.1	s__Acinetobacter venetianus	82.8167	736	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.49	96.30	0.89	0.81	21	-
GCF_900406815.1	s__Acinetobacter haemolyticus_A	82.451	701	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000369065.1	s__Acinetobacter haemolyticus	82.3516	687	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.85	97.09	0.87	0.81	55	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:49,968] [INFO] GTDB search result was written to GCF_014635545.1_ASM1463554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:49,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:49,973] [INFO] DFAST_QC result json was written to GCF_014635545.1_ASM1463554v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:49,974] [INFO] DFAST_QC completed!
[2024-01-24 13:32:49,974] [INFO] Total running time: 0h1m17s